Synthetic biochemistry molecular purge valve module that maintain co-factor balance

ABSTRACT

The disclosure provides a metabolic pathway for producing a metabolite, the metabolic pathway having a co-factor purge valve system for recycling a cofactor used in the metabolic pathway.

CROSS REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.15/127,351, filed Sep. 19, 2016, which claims priority to InternationalApplication No. PCT/US2015/024181, filed Apr. 2, 2015, which applicationclaims priority to U.S. Provisional Application Ser. No. 61/974,311,filed Apr. 2, 2014, the disclosures of which are incorporated herein byreference.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH

This invention was made with government support under Grant NumberDE-FC02-02ER63421, awarded by the U.S. Department of Energy. Thegovernment has certain rights in the invention.

TECHNICAL FIELD

The disclosure provides engineered pathways for chemical productionusing a cofactor balancing molecular purge system.

BACKGROUND

The greatest potential environmental benefit of metabolic engineeringwould be the production of low value/high volume commodity chemicals,such as biofuels. Yet the high yields required for the economicviability of low-value chemicals is particularly hard to achieve inmicrobes due to the myriad competing biochemical pathways needed forcell viability.

SUMMARY

The disclosure provides a recombinant, artificial or engineeredmetabolic pathway comprising a plurality of enzymatic steps thatconverts a substrate to a product, wherein the pathway includes anunbalanced production and utilization of a co-factor the pathwaycomprising a non-naturally occurring purge valve pathway that recyclesthe co-factor, wherein the purge valve pathway comprises an enzyme thatuses the co-factor to convert a metabolite in one or more of theplurality of enzymatic steps. In one embodiment, the recombinant,artificial or engineered metabolic pathway comprises (a) a firstenzymatic step that converts a first metabolite to a second metaboliteusing a first co-factor; (b) a second enzymatic step that converts thefirst metabolite to the second metabolite using a second co-factor; and(c) a third enzymatic step that converts the second or a thirdmetabolite to an intermediate or the product using the second cofactor;wherein when the co-factor utilization become unbalanced between thefirst and second cofactor, the purge valve pathway purges the excessco-factor. In a further embodiment of either of the foregoing theco-factors are oxidizing/reducing co-factors. In a further embodiment,the oxidizing/reducing co-factors are NAD⁺/NADH, NADP⁺/NADPH orFAD⁺/FADH. In another embodiment of any of the foregoing the firstcofactor comprises NAD⁺/NADH and the second cofactor comprisesNADP⁺/NADPH. In another embodiment of any of the foregoing the purgevalve pathway comprises a NADH dehydrogenase, and NADPH dehydrogenaseand an NADH oxidase. In a further embodiment, the NADH dehydrogenase isa NADH pyruvate dehydrogenase complex. In still a further embodiment,the NADH pyruvate dehydrogenase complex comprises a pyruvatedehydrogenase subunit a, a pyruvate dehydrogenase subunit b, adihydrolipoamide acetyltransferase, and a dihydrolipoamidedehydrogenase. In yet a further embodiment, the pyruvate dehydrogenasesubunit a comprises a sequence that is at least 90%, 91%, 92%, 93%, 94%,95%, 96%, 97%, 98%, 99% or 100% identical to SEQ ID NO:1, wherein thepyruvate dehydrogenase subunit b comprises a sequence that is at least90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical toSEQ ID NO:2, wherein the dihydrolipoamide acetyltransferase is at least90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical soSEQ ID NO:3, and wherein the dihydrolipoamide dehydrogenase is at least90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical toSEQ ID NO:5, wherein the complex converts pyruvate to acetyl-CoA. In yeta further embodiment, the NADPH dehydrogenase is a NADPH pyruvatedehydrogenase complex. In a further embodiment, the NADPH pyruvatedehydrogenase complex comprises a pyruvate dehydrogenase subunit a, apyruvate dehydrogenase subunit b, a dihydrolipoamide acetyltransferase,and a mutant dihydrolipoamide dehydrogenase the preferentially usesNADP⁺. In another embodiment, the pyruvate dehydrogenase subunit acomprises a sequence that is at least 90%, 91%, 92%, 93%, 94%, 95%, 96%,97%, 98%, 99% or 100% identical to SEQ ID NO:1, wherein the pyruvatedehydrogenase subunit b comprises a sequence that is at least 90%, 910,92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 100% identical to SEQ ID NO:2,wherein the dihydrolipoamide acetyltransferase is at least 900, 910,920, 930, 940, 950, 960, 970, 980, 990 or 100% identical so SEQ ID NO:3,and wherein the dihydrolipoamide dehydrogenase is at least 900, 910,920, 930, 940, 950, 960, 970, 980, 990 or 100% identical to SEQ ID NO:7and preferentially uses NADP⁺, wherein the complex converts pyruvate toacetyl-CoA. In yet further embodiments, the NADH oxidase is a NoxE orhomolog thereof. In a further embodiment, the NADH oxidase comprises asequence that is at least 900, 910, 920, 930, 940, 950, 960, 970, 980,990 or 100% identical to SEQ ID NO:10. In another embodiment of any ofthe foregoing the pathway is a cell-free system. In still anotherembodiment, the recombinant, artificial or engineered pathway producesPHB. In yet another embodiment, the recombinant, artificial orengineered pathway produces isoprene.

The disclosure also provides an enzymatic system comprising a metabolicpathway including a plurality of enzymes for converting a substrate to aproduct, the metabolic pathway having an unbalanced utilization ofreducing/oxidizing cofactors, wherein the enzymatic system comprises ametabolic purge valve comprising an NADH pyruvate dehydrogenase, andNADPH pyruvate dehydrogenase and a NADH/NADPH oxidase.

The disclosure also provides a recombinant microorganism comprising aheterologous NADH pyruvate dehydrogenase, a NADPH pyruvate dehydrogenaseand a NADH and/or NADPH oxidase.

The disclosure also provides a recombinant polypeptide comprising asequence that is at least 900, 910, 920, 930, 940, 950, 960, 970, 980,990 or 100% identical to SEQ ID NO:5 and comprising the mutations E206V,G207R, A208K, and S213R. In one embodiment, the polypeptide comprisesthe sequence of SEQ ID NO:7.

The disclosure also provides a polynucleotide encoding a polypeptidecomprising a sequence that is at least 900, 910, 920, 930, 940, 950,960, 970, 980, 990 or 100% identical to SEQ ID NO:5 and comprising themutations E206V, G207R, A208K, and S213R. In a further embodiment, thepolynucleotide encodes a polypeptide of SEQ ID NO:7. In a furtherembodiment, the polynucleotide comprises a sequence that is 70-90%, 91%,92%, 93%, 94%, 95%, 96%, 97%, 98%, 990 or 100% identical to SEQ ID NO:6and encodes a polypeptide of SEQ ID NO:7.

The disclosure provides a recombinant, artificial or engineered pathwaythat converts a substrate to a desired product, wherein the pathwayincludes an unbalanced production and utilization of a cofactor thepathway comprising a first metabolic step that produces a first reducedcofactor and a second metabolic step that oxidizes the first reducedcofactor, wherein the pathway comprises a purge valve pathway thatrecycles a second reduced cofactor. In one embodiment, the first reducedcofactor comprises NADPH and the second reduced cofactor comprises NADH.In a further embodiment, the purge valve pathway comprises a NADHdehydrogenase and an NADH oxidase. In still a further embodiment, theNADH dehydrogenase is a NADH pyruvate dehydrogenase. In anotherembodiment, the first reduced cofactor comprises NADH and the secondreduced cofactor comprises NADPH. In yet another embodiment, the purgevalve pathway comprises a NADPH dehydrogenase and an NADPH oxidase. In afurther embodiment, the NADPH dehydrogenase is a NADPH pyruvatedehydrogenase. In another embodiment of any of the foregoing claims thepathway produces isoprene from pyruvate. In yet another embodiment ofany of the foregoing claims the pathway produces PHB.

The details of one or more embodiments of the disclosure are set forthin the accompanying drawings and the description below. Other features,objects, and advantages will be apparent from the description anddrawings, and from the claims.

BRIEF DESCRIPTION OF THE DRAWINGS

The accompanying drawings, which are incorporated into and constitute apart of this specification, illustrate one or more embodiments of thedisclosure and, together with the detailed description, serve to explainthe principles and implementations of the invention.

FIG. 1A-C shows a synthetic biochemistry purge valve system for theproduction of PHB. (A) The in vitro metabolic pathway for the conversionof pyruvate to PHB. The pathway comprises 6 separate reactions: reaction1 (PDH^(NADH)), reaction 2 (PDH^(NADPH)), reaction 3 (NoxE), reaction 4(PhaA), reaction 5 (PhaB), reaction 6 (PhaC). The purge valve ishighlighted in the boxed pathway. (B) How the purge valve is designed tofunction. At low NADPH (high NADP+), PDH^(NADPH) reaction dominates,generating Acetyl-CoA and NADPH from pyruvate and NADP⁺. The purge valveis effectively “off”. In high NADPH (low NADP⁺) conditions, thePHD^(NADPH) enzyme is starved for oxidized cofactor, shutting down thepathway to Acetyl-CoA. In this situation, the PDH^(NADH)/NoxE systemtakes over, producing Acetyl-CoA; the purge valve is “on”. (C) Anexemplary chemical engineering schematic of the purge valve system usedin the production of PHB from pyruvate, involving a cofactor recycleloop.

FIG. 2 shows the design of the PDH^(NADPH) enzyme. The structures of thewild type G. stearothermophilus E3 subunit (E3, backbone trace) is shownoverlaid on the structure of E. coli glutathione reductase (GTX-NADPH,gray backbone trace). The NADPH substrate from glutathione reductase isshown in stick representation, showing the placement of the phosphatemoiety that needs to be accommodated. The residues changed to accept thephosphate (E206V, G207R, A208K, and S213R) are shown.

FIG. 3 shows the production of PHB using an optimized system. In thisreaction the production of PHB is monitored by an increase A₆₀₀ causedby precipitation of the PHB granules. No increase is seen in the absenceof the PHB polymerase, PhaC. The production of PHB is confirmed by a gaschromatography assay. The A₃₄₀ monitors the level of NADPH because noNADH is allowed to build up because of the presence of NoxE. The purgevalve system maintains a high level of NADPH throughout the reaction.

FIG. 4 shows a time course of pyruvate to PHB optimization reactionusing sub-optimal ratios of PDH^(NADPH) and PDH^(NADH). The A₃₄₀ traces,monitoring NADPH levels fall into three distinct phases. A fast initialreduction of NADPH by the PDH^(NADPH) is followed by a slow oxidation ofNADPH by PhaB as the intermediate levels rise. As the reaction proceeds,the purge valve turns off and NADPH levels rise again. The evolution ofthe system coincides with the increase at A₆₀₀ which represents theprecipitation of the PHB granules from solution.

FIG. 5A-B shows the purge valve system is robust. (A) The graph showsrelative yield of PHB upon starting with different amounts of each ofthe cofactors. The relative yields represent the ratio of the final A₆₀₀for the reaction, relative to the final A₆₀₀ for the optimized reaction.All reactions show a relatively robust yield in comparison to thenegative control lacking the final phaC enzyme (orange bar). The errorbars reflect the standard deviation of three independent reactions. (B)Table of the numbers reflected in the graph in part A.

FIG. 6A-B shows employment of the purge valve for the production ofisoprene. (A) The in vitro metabolic pathway for the conversion ofpyruvate to isoprene. The purge valve highlighted in the box comprisingthe same enzymes/reactions as in FIG. 1A. In the mevalonate pathway, 3Acetyl-CoA are used to make HMG-CoA (enzymes 6 and 7). HMG-CoA isreduced by HMGR (enzyme 8) with 2 NADPH to give mevalonate. 3 ATP arethen used to convert mevalonate to isopentenyl pyrophosphate followed byproduction of isoprene (enzymes 9-12). (B) The graph shows thedependence of isoprene production on the purge valve. No purge valve wasused in the first reaction (PDH^(NADH), NADPH, NoxE). NADPH was simplyadded and NADH recycled using NoxE. The final experiment (PDH^(NADH),PDH^(NADPH), NoxE) shows results employing the full purge valve system.Leaving out any component of the purge valve system resulted in dramaticdecreases in isoprene production. Each reaction was performed induplicate.

FIG. 7 shows the stability of the GsPDH enzymes. Enzymes were incubatedat a given temperature for 1 hour and then immediately assayed foractivity.

FIG. 8 shows the stability of the PHB system at room temperature. Allthe components of the optimized PHB system were mixed, leaving outpyruvate and then the system was incubated at room temperature. Atvarious times the reaction was initiated by the addition of pyruvate andthe extent of the reaction monitored by the final OD₆₀₀. The plot showsthe percent extent of reaction achieved for each pre-incubation time.

DETAILED DESCRIPTION

As used herein and in the appended claims, the singular forms “a,”“and,” and “the” include plural referents unless the context clearlydictates otherwise. Thus, for example, reference to “a polynucleotide”includes a plurality of such polynucleotides and reference to “theenzyme” includes reference to one or more enzymes, and so forth.

Unless defined otherwise, all technical and scientific terms used hereinhave the same meaning as commonly understood to one of ordinary skill inthe art to which this disclosure belongs. Although methods and materialssimilar or equivalent to those described herein can be used in thepractice of the disclosed methods and compositions, the exemplarymethods, devices and materials are described herein.

Also, the use of “or” means “and/or” unless stated otherwise. Similarly,“comprise,” “comprises,” “comprising” “include,” “includes,” and“including” are interchangeable and not intended to be limiting.

It is to be further understood that where descriptions of variousembodiments use the term “comprising,” those skilled in the art wouldunderstand that in some specific instances, an embodiment can bealternatively described using language “consisting essentially of” or“consisting of.”

Any publications discussed above and throughout the text are providedsolely for their disclosure prior to the filing date of the presentapplication. Nothing herein is to be construed as an admission that theinventors are not entitled to antedate such disclosure by virtue ofprior disclosure.

As used herein, an “activity” of an enzyme is a measure of its abilityto catalyze a reaction resulting in a metabolite, i.e., to “function”,and may be expressed as the rate at which the metabolite of the reactionis produced. For example, enzyme activity can be represented as theamount of metabolite produced per unit of time or per unit of enzyme(e.g., concentration or weight), or in terms of affinity or dissociationconstants.

The term “biosynthetic pathway”, also referred to as “metabolicpathway”, refers to a set of anabolic or catabolic biochemical reactionsfor converting (transmuting) one chemical species into another. Geneproducts belong to the same “metabolic pathway” if they, in parallel orin series, act on the same substrate, produce the same product, or acton or produce a metabolic intermediate (i.e., metabolite) between thesame substrate and metabolite end product. The disclosure provides invitro biosynthetic pathways comprising a metabolic purge vale as well asproviding recombinant microorganism having a metabolically engineeredpathway comprising a metabolic purge valve for the production of adesired product or intermediate.

As used herein a “cofactor” generally refers to a chemical compound ormetabolite that is required for a protein's biological activity. Theseproteins are commonly enzymes, and cofactors assist in biochemicaltransformations. Cofactors include, but are not limited to, one or moreinorganic ions, or a complex organic or metalloorganic moleculesometimes referred to as a coenzyme; most of which are derived fromvitamins and from required organic nutrients in small amounts. Someenzymes or enzyme complexes require several cofactors. For example, themultienzyme complex pyruvate dehydrogenase at the junction of glycolysisand the citric acid cycle requires five organic cofactors and one metalion: loosely bound thiamine pyrophosphate (TPP), covalently boundlipoamide and flavin adenine dinucleotide (FAD), and the cosubstratesnicotinamide adenine dinucleotide (NAD⁺) and coenzyme A (CoA), and ametal ion (Mg²⁺). Organic cofactors are often vitamins or are made fromvitamins. Many contain the nucleotide adenosine monophosphate (AMP) aspart of their structures, such as ATP, coenzyme A, FAD, and NAD⁺.

An “enzyme” means any substance, typically composed wholly or largely ofamino acids making up a protein or polypeptide that catalyzes orpromotes, more or less specifically, one or more chemical or biochemicalreactions.

The term “expression” with respect to a gene or polynucleotide refers totranscription of the gene or polynucleotide and, as appropriate,translation of the resulting mRNA transcript to a protein orpolypeptide. Thus, as will be clear from the context, expression of aprotein or polypeptide results from transcription and translation of theopen reading frame.

A “metabolite” refers to any substance produced by metabolism or asubstance necessary for or taking part in a particular metabolic processthat gives rise to a desired metabolite, chemical, alcohol or ketone. Ametabolite can be an organic compound that is a starting material (e.g.,a carbohydrate, a sugar phosphate, pyruvate etc.), an intermediate in(e.g., acetyl-coA), or an end product (e.g., isoprene or PHB) ofmetabolism. Metabolites can be used to construct more complex molecules,or they can be broken down into simpler ones. Intermediate metabolitesmay be synthesized from other metabolites, perhaps used to make morecomplex substances, or broken down into simpler compounds, often withthe release of chemical energy.

As used herein, the term “metabolically engineered” or “metabolicengineering” involves rational pathway design and assembly ofbiosynthetic genes, genes associated with operons, and control elementsof such polynucleotides, for the production of a desired metabolite,such as acetyl-CoA, higher alcohols or other chemical, in amicroorganism or in vitro. “Metabolically engineered” can furtherinclude optimization of metabolic flux by regulation and optimization oftranscription, translation, protein stability and protein functionalityusing genetic engineering and appropriate culture condition includingthe reduction of, disruption, or knocking out of, a competing metabolicpathway that competes with an intermediate leading to a desired pathway.A biosynthetic gene can be heterologous to the host microorganism,either by virtue of being foreign to the host, or being modified bymutagenesis, recombination, and/or association with a heterologousexpression control sequence in an endogenous host cell. In oneembodiment, where the polynucleotide is xenogenetic to the hostorganism, the polynucleotide can be codon optimized.

A “metabolic purge valve” refers to an engineered metabolic pathway that‘purges’ excess metabolites and/or co-factors resulting in a recyclingof the metabolite or co-factor for use in a primary metabolic pathway.

The term “polynucleotide,” “nucleic acid” or “recombinant nucleic acid”refers to polynucleotides such as deoxyribonucleic acid (DNA), and,where appropriate, ribonucleic acid (RNA).

A “protein” or “polypeptide”, which terms are used interchangeablyherein, comprises one or more chains of chemical building blocks calledamino acids that are linked together by chemical bonds called peptidebonds. A protein or polypeptide can function as an enzyme.

The term “recombinant microorganism” and “recombinant host cell” areused interchangeably herein and refer to microorganisms that have beengenetically modified to express or over-express endogenouspolynucleotides, or to express non-endogenous sequences, such as thoseincluded in a vector. The polynucleotide generally encodes a targetenzyme involved in a metabolic pathway for producing a desiredmetabolite as described herein, but may also include protein factorsnecessary for regulation or activity or transcription. Accordingly,recombinant microorganisms described herein have been geneticallyengineered to express or over-express target enzymes not previouslyexpressed or over-expressed by a parental microorganism. It isunderstood that the terms “recombinant microorganism” and “recombinanthost cell” refer not only to the particular recombinant microorganismbut to the progeny or potential progeny of such a microorganism.

The term “substrate” or “suitable substrate” refers to any substance orcompound that is converted or meant to be converted into anothercompound by the action of an enzyme. The term includes not only a singlecompound, but also combinations of compounds, such as solutions,mixtures and other materials which contain at least one substrate, orderivatives thereof. Further, the term “substrate” encompasses not onlycompounds that provide a carbon source suitable for use as a startingmaterial, but also intermediate and end product metabolites used in apathway as described herein. In addition, a substrate can be an oxidizedor reduced co-factor or a factor that is phosphorylated orde-phosphorylated.

Metabolic engineering and synthetic biology have been employed for theproduction of high value chemicals but have not been as successful ashoped in meeting the stringent economics of large scale commoditychemical manufacturing. Microbial systems are often hampered by avariety of technical challenges that make it hard to achieve costcompetitiveness, including poor yields due to competing pathways; lowproductivity caused by slow growth rates or difficulties in pathwayoptimization; contaminating microbial growth; product toxicity; andexpensive product isolation.

One approach that is beginning to receive attention is to performcomplex biochemical transformations using mixtures of enzymes in areaction vessel or flow system rather than within a cell. Buildingsingle, dedicated pathways in vitro can eliminate side reactions thatoccur in the cell, so that nearly 100% yields and fast reaction timesare possible. In vitro biochemical systems also allow for more precisecontrol over optimization and product toxicity problems can be moreeasily diagnosed and mitigated. Moreover, product extraction can be morefacile.

Traditionally, in vitro pathway construction has been relegated to useas a research tool or in applications that require only 1-3 enzymes forthe production of chiral compounds and other high value chemicals.Improvements in protein expression and access to stable enzymes havemade more complex systems possible. In vitro biotransformation systemshave been reported in recent years involving systems of over thirtyenzymes. One of the first modern studies in this area was an artificialpathway that produced hydrogen from starch. The concept was recentlyadvanced with a creative system that generated hydrogen from cellobioseat nearly 100% yields. In another effort, hyper-thermophilic glycolysisenzymes were heterologously expressed, heat purified, and assembled toconvert glucose to n-butanol in 82% yield. In another study, anelegantly simplified non-phosphorylative Entner-Doudoroff pathway fromhyper-thermophilic archaea was constructed to produce ethanol andisobutanol in 55% yields. These pioneering studies illustrate theflexibility of synthetic biochemistry and the potential for high yields.

Maintaining proper cofactor balance is an essential part of generatingflux and providing a driving force through an enzymatic pathway. Invivo, the enzymatic specificity for the cofactors NADH and NADPH aretypically used to control the carbon flux through catabolic and anabolicpathways respectively. Organisms typically sense the reduction state ofthese cofactors and use this information to up-regulate or down-regulatecatabolic and anabolic pathways to cope with environmental changes. Invitro systems, however, do not have the myriad of peripheral pathwaysthat facilitate this control. Moreover, the natural anabolic andcatabolic specificities for NADH and NADPH complicate in vitrobiotransformations. Synthetic biochemistry systems have often dealt withthese problems by careful considerations of cofactor stoichiometry inpathway design, through the use of expensive sacrificial metabolites,reengineering enzymes so that only a single cofactor type is needed,adding excess cofactors, or constantly adding intermediates to thereaction mix to sustain the process.

Although the methods, compositions and systems described herein aredescribed with reference to certain metabolic products, the methods,compositions and systems are applicable to a broad range of recombinantbiochemical pathways were co-factor recycling is important. In oneexemplary engineered pathway the disclosure describes the production ofpolyhydroxybutyrates (PHBs) and polyhydroxyalkanoates (PHAs). In anotherexemplary embodiment, the disclosure describes the production ofisoprene. Both embodiments utilize a molecular purge valve system of thedisclosure to maintain appropriate co-factor balance.

PHBs and other PHAs are biodegradable thermoplastics. PHAs can havecharacteristics similar to many popular petrochemical derived polymers,but are nontoxic and biodegradable, thus these compositions areattracting increased attention as a possible green alternative topetroleum based polymers in a wide range of applications. The bestcharacterized and most abundant PHA polymer is polyhydroxybutyrate (PHB)that is naturally produced from Acetyl-CoA as a carbon and energystorage mechanism in many organisms. Currently, industrial production ofPHB is done by in vivo batch culture processes under nutrientstarvation. This process is typically very time consuming, requireslarge fermentation volumes, and requires expensive methods for theextraction of PHB. Prior attempts to produce bioplastic in vitro haverequired the addition of sacrificial substrates and a molar excess ofcofactors to convert acetate to PHB.

Isoprene is a platform chemical for a variety of products, but it ismostly employed in the production of synthetic rubber. The isoprenoidpathway also provides precursors for over 25,000 known biomoleculesincluding drugs such as taxol and potential biofuels. There have been anumber of efforts to produce isoprene in microorganisms and the bestreported yield is 28% from glucose. Korman et al. (Protein Sci.,23(5):576-85, May 2014), showed that a synthetic biochemistry systemcould produce isoprene in >95% yield from pyruvate as long as highenergy cofactors were added. Examples of isoprenoids that can beproduced by the methods, compositions and systems of the disclosure areselected from the group consisting of a hemiterpene, monoterpene,diterpene, triterpene, tetraterpene, sesquiterpene, and polyterpene. Forexample, the isoprenoid can be selected from the group consisting ofabietadiene, amorphadiene, carene, α-farnesene, β-farnesene, farnesol,geraniol, geranylgeraniol, isoprene, linalool, limonene, myrcene,nerolidol, ocimene, patchoulol, β-pinene, sabinene, γ-terpinene,terpinolene, and valencene.

The disclosure describes a purge valve system for co-factor balance inin vitro pathways for chemical production and in vivo systems. Forexample, the disclosure describes a pathway to convert pyruvate into PHBthat maintains sustainable reducing cofactor balance, without therequirement for perfect stoichiometric matching of cofactor generationand usage to carbon usage. Further, the disclosure described the use ofthe molecular purge valve system in other pathways. For example, thedisclosure demonstrates the purge valve system can be used as the basisfor the production of other Acetyl-CoA derived products by applying itto the production of isoprene from pyruvate via the mevalonate pathway.Thus, the regulatory modules described herein can free us from having toperfectly balance cofactor utilization when designing syntheticbiochemistry systems.

The disclosure provides a robust node of control to balance theproduction and consumption of cofactors such as NADPH and NADH in aself-regulating and self-balancing manner. This in vitro pathwaymaintains cofactor balance without requiring adherence to stoichiometryin the generation and utilization of cofactors to ensure carbon flux. Inpart because the system can sustain high levels of NADPH, driving thetransformation to near completion, converting for example, pyruvate toeither PHB or isoprene at nearly 100% of the theoretical yield.Moreover, the high yields in the system are robust to 10-fold variationsin cofactor levels.

Ultimately the methods and compositions of the disclosure can beexpanded to incorporate the conversion of low cost substrates such asglucose or other sugars into pyruvate, which would involve theglycolysis pathway or parts of the glycolysis pathway. Indeed asynthetic biochemistry system employing glycolysis has been demonstratedpreviously. Building more complex compounds from Acetyl-CoA such asfatty acids, polyketides, and other isoprenoids incorporate the use andrecycling of ATP. In such instances developing a regulatory systems likethe purge valve employed here, will free synthetic biochemistry systemdesign from having to consume the high energy cofactors during theanabolic phase in perfect stoichiometric balance. Thus, the approach canhelp diversify the chemical targets of synthetic biochemistry.

The biotransformation of pyruvate into PHB, illustrates a basicco-factor imbalance problem that is encountered in biochemical systems.In particular, conversion of pyruvate to Acetyl-CoA by pyruvatedehydrogenase (PDH) yields one molecule of NADH. However, the threeenzyme pathway (phaA, B, and C) to PHB from Acetyl-CoA utilizes only onehalf a molecule of NADPH per Acetyl-CoA. Thus, the canonical pathwayproduces an excess of reducing equivalents. Moreover, the reducingequivalents are of the wrong type (NADH rather than NADPH). Thedisclosure exemplifies the purge valve system in a pathway for theregulation of NAD and NADP and their reduced equivalents, shown in FIG.1A, that can generate the correct cofactor and regulate its production.

In the design, a synthetic biochemistry “purge valve” was developed thateffectively decouples the stoichiometric production of NAD(P)H fromAcetyl-CoA (FIG. 1). To this end a mixture of both an NAD⁺-utilizingwild-type PDH (PDH^(NADH)), a mutant PDH that utilizes NADP⁺(PDH^(NADPH)), and a water generating NADH oxidase (NoxE) thatspecifically oxidizes NADH, but not NADPH was utilized. By employingthis metabolic node, NADPH was generated for PHB production frompyruvate, but also dissipate excess reducing equivalents in anauto-regulatory manner. As illustrated in FIG. 1B, under low NADPH, highNADP⁺ conditions, the mutant PDH^(NADPH) can operate to generateAcetyl-CoA and restore NADPH levels. Under high NADPH, low NADP⁺conditions, the PDH^(NADPH) activity will automatically be choked off,and the wild-type PDH^(NADH) will be used preferentially to produceAcetyl-CoA and NADH. In this high NADPH condition, the reducingequivalents are not needed. Because the reducing equivalents areproduced in the form of NADH and not NADPH, they are eliminated by anoxidase, NoxE. The presence of NoxE ensures that NADH never builds upand the PDH^(NADH) can always operate to generate carbon for the PHBpathway in the form of Acetyl-CoA. The PDH^(NADH)/PDH^(NADPH)/NoxEsystem acts like a purge valve that opens under conditions of high NADPHto relieve the excess reducing equivalent “pressure” (i.e. buildup ofNADH) and allow carbon flux to be maintained. An engineering schematicof the purge valve system is shown in FIG. 1C.

For example, the disclosure demonstrates that to construct an in vitrosystem the enzymes were acquired commercially or purified, tested foractivity, and mixed together in a properly selected reaction buffer. Thesystem comprises a core set of enzymes for the “purge valve” system anda secondary set of enzyme for the synthesis of a desired chemical orbiofuel. The core purge valve system can be utilized in combination withany in vitro system that converts one set of metabolites (e.g., a firstcarbon source) to a second metabolite (e.g., a desired chemicalproduct), wherein the secondary metabolic pathway (e.g., the productpathway) uses or produces and excess of co-factor metabolites (e.g.,produces an excess of reducing equivalents). In such instances a purgevalve system can be utilized to balance the cofactors. For example, inthe case of PHB and isoprene these reducing equivalents can be utilizedand optimized. In one embodiment, the metabolic pathway produces anexcess of a reducing equivalent that is needed for production of thedesired product. For example, in Scheme 1, below, a first metabolic stepproduces reducing equivalents and a second metabolic step utilizes thereducing equivalents, however, the second step uses only a fraction ofthe reducing equivalents produced in the first step. Thus, in a closedsystem, the limiting factor will be the reducing equivalents.

Upon utilization of the available NADP⁺ in scheme 1, for example, thesystem would stop and no further metabolites (“B” or “X”) would be made.However, in the purge valve system of the disclosure, a secondarypathway that can oxidize the reducing equivalents would become activeand allow production of A to B, while still allowing use of the NADPH insteps B to X. Once sufficient enough NADP+ is present then the metabolicpathway from A to B would use the NADP⁺.

In one embodiment, the purge valve for use in an in vitro systemcomprises: a combination of both an NADH-dehydrogenase enzyme and anNADPH-dehydrogenase and a NADH or NADPH-oxidase. In one embodiment, thepurge valve system comprises an NADH-pyruvate dehydrogenase complex, anNADPH-pyruvate dehydrogenase complex and an NADH-oxidase. It should benoted that other dehydrogenase pairs can be used.

The purge valve system of the foregoing embodiment can be used incombination with any metabolic pathway that produces NADH or NADPH andutilizes a fraction of what was produced in the production of a desiredproduct. For example, the purge system can be used in a pathway thatconverts pyruvate to acetyl-CoA to produce NADH or NADPH and thatutilizes NADH or NADPH to further produce a desired metabolite.Exemplary pathways include the PHB and isoprene pathways describedbelow.

The disclosure provides pathways that can be developed in vitro in anumber of ways. For example, the desired enzymes can becloned/engineered into a microorganism or cell, expressed and thenpurified from the culture. In another example, the enzymes can beexpressed, the cells disrupted and a disrupted preparation used in thepathways of the disclosure. In another embodiment, the enzymes can bepurified and tethered to a substrate in a system (e.g., in amicrofluidic system) for use in the metabolic pathway. In yet anotherembodiment, thermophilic enzymes having the desired activity can becloned, expressed and the cell or preparations therefrom heated to atemperature wherein the desired enzymes remain active while undesiredenzymes are denatured. In yet another embodiment, the enzymes can becommercially purchased and mixed as appropriate. In all of the foregoingembodiments, the system would be combined with the necessary substratesand cofactors (e.g., NAD⁻, NADP⁻, FAD⁻, AMP, ADP, ATP and the like).

Accordingly, the disclosure provides “engineered” or “modified”microorganisms that are produced via the introduction of geneticmaterial into a host or parental microorganism of choice therebymodifying or altering the cellular physiology and biochemistry of themicroorganism. Through the introduction of genetic material the parentalmicroorganism acquires new properties, e.g. the ability to produce anew, or greater quantities of, an intracellular metabolite. The geneticmaterial introduced into the parental microorganism contains gene(s), orparts of gene(s), coding for one or more of the enzymes involved in abiosynthetic pathway and include gene(s), or parts of gene(s), codingfor one or more of the enzymes involved in a metabolic purge valve, thepathway(s) useful for the production of a desired metabolite (e.g.,acetyl-phosphate and/or acetyl-CoA), and may also include additionalelements for the expression and/or regulation of expression of thesegenes, e.g. promoter sequences.

An engineered or modified microorganism can also include in thealternative or in addition to the introduction of a genetic materialinto a host or parental microorganism, the disruption, deletion orknocking out of a gene or polynucleotide to alter the cellularphysiology and biochemistry of the microorganism. Through the reduction,disruption or knocking out of a gene or polynucleotide the microorganismacquires new or improved properties (e.g., the ability to produce a newor greater quantities of an intracellular metabolite, improve the fluxof a metabolite down a desired pathway, and/or reduce the production ofundesirable by-products). For example, it may be desirable to engineeran organism to express a desired set for enzymes in a metabolic pathwaywhile eliminating enzymes of competing pathways. This engineering can beapplicable for both in vitro (where upon disruption or purificationundesirable enzymes are not present) or in vivo.

A “native” or “wild-type” protein, enzyme, polynucleotide, gene, orcell, means a protein, enzyme, polynucleotide, gene, or cell that occursin nature.

A “parental microorganism” refers to a cell used to generate arecombinant microorganism. The term “parental microorganism” describes,in one embodiment, a cell that occurs in nature, i.e. a “wild-type” cellthat has not been genetically modified. The term “parentalmicroorganism” further describes a cell that serves as the “parent” forfurther engineering. In this latter embodiment, the cell may have beengenetically engineered, but serves as a source for further geneticengineering.

For example, a wild-type microorganism can be genetically modified toexpress or over express a first target enzyme such as a NADH-pyruvatedehydrogenase. This microorganism can act as a parental microorganism inthe generation of a microorganism modified to express or over-express asecond target enzyme e.g., a NADH-oxidase. As used herein, “express” or“over express” refers to the phenotypic expression of a desired geneproduct. In one embodiment, a naturally occurring gene in the organismcan be engineered such that it is linked to a heterologous promoter orregulatory domain, wherein the regulatory domain causes expression ofthe gene, thereby modifying its normal expression relative to thewild-type organism. Alternatively, the organism can be engineered toremove or reduce a repressor function on the gene, thereby modifying itsexpression. In yet another embodiment, a cassette comprising the genesequence operably linked to a desired expression control/regulatoryelement is engineered in to the microorganism.

Accordingly, a parental microorganism functions as a reference cell forsuccessive genetic modification events. Each modification event can beaccomplished by introducing one or more nucleic acid molecules in to thereference cell. The introduction facilitates the expression orover-expression of one or more target enzyme or the reduction orelimination of one or more target enzymes. It is understood that theterm “facilitates” encompasses the activation of endogenouspolynucleotides encoding a target enzyme through genetic modification ofe.g., a promoter sequence in a parental microorganism. It is furtherunderstood that the term “facilitates” encompasses the introduction ofexogenous polynucleotides encoding a target enzyme in to a parentalmicroorganism.

Polynucleotides that encode enzymes useful for generating metabolitesincluding homologs, variants, fragments, related fusion proteins, orfunctional equivalents thereof, are used in recombinant nucleic acidmolecules that direct the expression of such polypeptides in appropriatehost cells, such as bacterial or yeast cells.

The sequence listing appended hereto provide exemplary polynucleotidesequences encoding polypeptides useful in the methods described herein.It is understood that the addition of sequences which do not alter theencoded activity of a nucleic acid molecule, such as the addition of anon-functional or non-coding sequence (e.g., polyHIS tags), is aconservative variation of the basic nucleic acid.

It is understood that a polynucleotide described above include “genes”and that the nucleic acid molecules described above include “vectors” or“plasmids.” Accordingly, the term “gene”, also called a “structuralgene” refers to a polynucleotide that codes for a particular polypeptidecomprising a sequence of amino acids, which comprise all or part of oneor more proteins or enzymes, and may include regulatory(non-transcribed) DNA sequences, such as promoter region or expressioncontrol elements, which determine, for example, the conditions underwhich the gene is expressed. The transcribed region of the gene mayinclude untranslated regions, including introns, 5′-untranslated region(UTR), and 3′-UTR, as well as the coding sequence.

Those of skill in the art will recognize that, due to the degeneratenature of the genetic code, a variety of codons differing in theirnucleotide sequences can be used to encode a given amino acid. Aparticular polynucleotide or gene sequence encoding a biosyntheticenzyme or polypeptide described above are referenced herein merely toillustrate an embodiment of the disclosure, and the disclosure includespolynucleotides of any sequence that encode a polypeptide comprising thesame amino acid sequence of the polypeptides and proteins of the enzymesutilized in the methods of the disclosure. In similar fashion, apolypeptide can typically tolerate one or more amino acid substitutions,deletions, and insertions in its amino acid sequence without loss orsignificant loss of a desired activity. The disclosure includes suchpolypeptides with alternate amino acid sequences, and the amino acidsequences encoded by the DNA sequences shown herein merely illustrateexemplary embodiments of the disclosure.

The disclosure provides polynucleotides in the form of recombinant DNAexpression vectors or plasmids, as described in more detail elsewhereherein, that encode one or more target enzymes. Generally, such vectorscan either replicate in the cytoplasm of the host microorganism orintegrate into the chromosomal DNA of the host microorganism. In eithercase, the vector can be a stable vector (i.e., the vector remainspresent over many cell divisions, even if only with selective pressure)or a transient vector (i.e., the vector is gradually lost by hostmicroorganisms with increasing numbers of cell divisions). Thedisclosure provides DNA molecules in isolated (i.e., not pure, butexisting in a preparation in an abundance and/or concentration not foundin nature) and purified (i.e., substantially free of contaminatingmaterials or substantially free of materials with which thecorresponding DNA would be found in nature) form.

A polynucleotide of the disclosure can be amplified using cDNA, mRNA oralternatively, genomic DNA, as a template and appropriateoligonucleotide primers according to standard PCR amplificationtechniques and those procedures described in the Examples section below.The nucleic acid so amplified can be cloned into an appropriate vectorand characterized by DNA sequence analysis. Furthermore,oligonucleotides corresponding to nucleotide sequences can be preparedby standard synthetic techniques, e.g., using an automated DNAsynthesizer.

It is also understood that an isolated polynucleotide molecule encodinga polypeptide homologous to the enzymes described herein can be createdby introducing one or more nucleotide substitutions, additions ordeletions into the nucleotide sequence encoding the particularpolypeptide, such that one or more amino acid substitutions, additionsor deletions are introduced into the encoded protein. Mutations can beintroduced into the polynucleotide by standard techniques, such assite-directed mutagenesis and PCR-mediated mutagenesis. In contrast tothose positions where it may be desirable to make a non-conservativeamino acid substitution, in some positions it is preferable to makeconservative amino acid substitutions.

As will be understood by those of skill in the art, it can beadvantageous to modify a coding sequence to enhance its expression in aparticular host. The genetic code is redundant with 64 possible codons,but most organisms typically use a subset of these codons. The codonsthat are utilized most often in a species are called optimal codons, andthose not utilized very often are classified as rare or low-usagecodons. Codons can be substituted to reflect the preferred codon usageof the host, a process sometimes called “codon optimization” or“controlling for species codon bias.”

Optimized coding sequences containing codons preferred by a particularprokaryotic or eukaryotic host (see also, Murray et al. (1989) Nucl.Acids Res. 17:477-508) can be prepared, for example, to increase therate of translation or to produce recombinant RNA transcripts havingdesirable properties, such as a longer half-life, as compared withtranscripts produced from a non-optimized sequence. Translation stopcodons can also be modified to reflect host preference. For example,typical stop codons for S. cerevisiae and mammals are UAA and UGA,respectively. The typical stop codon for monocotyledonous plants is UGA,whereas insects and E. coli commonly use UAA as the stop codon (Dalphinet al. (1996) Nucl. Acids Res. 24: 216-218). Methodology for optimizinga nucleotide sequence for expression in a plant is provided, forexample, in U.S. Pat. No. 6,015,891, and the references cited therein.

“Transformation” refers to the process by which a vector is introducedinto a host cell. Transformation (or transduction, or transfection), canbe achieved by any one of a number of means including electroporation,microinjection, biolistics (or particle bombardment-mediated delivery),or agrobacterium mediated transformation.

A “vector” generally refers to a polynucleotide that can be propagatedand/or transferred between organisms, cells, or cellular components.Vectors include viruses, bacteriophage, pro-viruses, plasmids,phagemids, transposons, and artificial chromosomes such as YACs (yeastartificial chromosomes), BACs (bacterial artificial chromosomes), andPLACs (plant artificial chromosomes), and the like, that are “episomes,”that is, that replicate autonomously or can integrate into a chromosomeof a host cell. A vector can also be a naked RNA polynucleotide, a nakedDNA polynucleotide, a polynucleotide composed of both DNA and RNA withinthe same strand, a poly-lysine-conjugated DNA or RNA, apeptide-conjugated DNA or RNA, a liposome-conjugated DNA, or the like,that are not episomal in nature, or it can be an organism whichcomprises one or more of the above polynucleotide constructs such as anagrobacterium or a bacterium.

The various components of an expression vector can vary widely,depending on the intended use of the vector and the host cell(s) inwhich the vector is intended to replicate or drive expression.Expression vector components suitable for the expression of genes andmaintenance of vectors in E. coli, yeast, Streptomyces, and othercommonly used cells are widely known and commercially available. Forexample, suitable promoters for inclusion in the expression vectors ofthe disclosure include those that function in eukaryotic or prokaryotichost microorganisms. Promoters can comprise regulatory sequences thatallow for regulation of expression relative to the growth of the hostmicroorganism or that cause the expression of a gene to be turned on oroff in response to a chemical or physical stimulus. For E. coli andcertain other bacterial host cells, promoters derived from genes forbiosynthetic enzymes, antibiotic-resistance conferring enzymes, andphage proteins can be used and include, for example, the galactose,lactose (lac), maltose, tryptophan (trp), beta-lactamase (bla),bacteriophage lambda PL, and T5 promoters. In addition, syntheticpromoters, such as the tac promoter (U.S. Pat. No. 4,551,433, which isincorporated herein by reference in its entirety), can also be used. ForE. coli expression vectors, it is useful to include an E. coli origin ofreplication, such as from pUC, p1P, p1, and pBR.

Thus, recombinant expression vectors contain at least one expressionsystem, which, in turn, is composed of at least a portion of a genecoding sequences operably linked to a promoter and optionallytermination sequences that operate to effect expression of the codingsequence in compatible host cells. The host cells are modified bytransformation with the recombinant DNA expression vectors of thedisclosure to contain the expression system sequences either asextrachromosomal elements or integrated into the chromosome.

In addition, and as mentioned above, homologs of enzymes useful forgenerating metabolites are encompassed by the microorganisms and methodsprovided herein. The term “homologs” used with respect to an originalenzyme or gene of a first family or species refers to distinct enzymesor genes of a second family or species which are determined byfunctional, structural or genomic analyses to be an enzyme or gene ofthe second family or species which corresponds to the original enzyme orgene of the first family or species. Most often, homologs will havefunctional, structural or genomic similarities. Techniques are known bywhich homologs of an enzyme or gene can readily be cloned using geneticprobes and PCR. Identity of cloned sequences as homolog can be confirmedusing functional assays and/or by genomic mapping of the genes.

A protein has “homology” or is “homologous” to a second protein if thenucleic acid sequence that encodes the protein has a similar sequence tothe nucleic acid sequence that encodes the second protein.Alternatively, a protein has homology to a second protein if the twoproteins have “similar” amino acid sequences. (Thus, the term“homologous proteins” is defined to mean that the two proteins havesimilar amino acid sequences).

As used herein, two proteins (or a region of the proteins) aresubstantially homologous when the amino acid sequences have at leastabout 30%, 40%, 50% 60%, 65%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%,94%, 95%, 96%, 97%, 98%, or 99% identity. To determine the percentidentity of two amino acid sequences, or of two nucleic acid sequences,the sequences are aligned for optimal comparison purposes (e.g., gapscan be introduced in one or both of a first and a second amino acid ornucleic acid sequence for optimal alignment and non-homologous sequencescan be disregarded for comparison purposes). In one embodiment, thelength of a reference sequence aligned for comparison purposes is atleast 30%, typically at least 40%, more typically at least 50%, evenmore typically at least 60%, and even more typically at least 70%, 80%,90%, 100% of the length of the reference sequence. The amino acidresidues or nucleotides at corresponding amino acid positions ornucleotide positions are then compared. When a position in the firstsequence is occupied by the same amino acid residue or nucleotide as thecorresponding position in the second sequence, then the molecules areidentical at that position (as used herein amino acid or nucleic acid“identity” is equivalent to amino acid or nucleic acid “homology”). Thepercent identity between the two sequences is a function of the numberof identical positions shared by the sequences, taking into account thenumber of gaps, and the length of each gap, which need to be introducedfor optimal alignment of the two sequences.

When “homologous” is used in reference to proteins or peptides, it isrecognized that residue positions that are not identical often differ byconservative amino acid substitutions. A “conservative amino acidsubstitution” is one in which an amino acid residue is substituted byanother amino acid residue having a side chain (R group) with similarchemical properties (e.g., charge or hydrophobicity). In general, aconservative amino acid substitution will not substantially change thefunctional properties of a protein. In cases where two or more aminoacid sequences differ from each other by conservative substitutions, thepercent sequence identity or degree of homology may be adjusted upwardsto correct for the conservative nature of the substitution. Means formaking this adjustment are well known to those of skill in the art (see,e.g., Pearson et al., 1994, hereby incorporated herein by reference).

In some instances “isozymes” can be used that carry out the samefunctional conversion/reaction, but which are so dissimilar in structurethat they are typically determined to not be “homologous”.

A “conservative amino acid substitution” is one in which the amino acidresidue is replaced with an amino acid residue having a similar sidechain. Families of amino acid residues having similar side chains havebeen defined in the art. These families include amino acids with basicside chains (e.g., lysine, arginine, histidine), acidic side chains(e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g.,glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine),nonpolar side chains (e.g., alanine, valine, leucine, isoleucine,proline, phenylalanine, methionine, tryptophan), beta-branched sidechains (e.g., threonine, valine, isoleucine) and aromatic side chains(e.g., tyrosine, phenylalanine, tryptophan, histidine). The followingsix groups each contain amino acids that are conservative substitutionsfor one another: 1) Serine (S), Threonine (T); 2) Aspartic Acid (D),Glutamic Acid (E); 3) Asparagine (N), Glutamine (Q); 4) Arginine (R),Lysine (K); 5) Isoleucine (I), Leucine (L), Methionine (M), Alanine (A),Valine (V), and 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W).

Sequence homology for polypeptides, which can also be referred to aspercent sequence identity, is typically measured using sequence analysissoftware. See, e.g., the Sequence Analysis Software Package of theGenetics Computer Group (GCG), University of Wisconsin BiotechnologyCenter, 910 University Avenue, Madison, Wis. 53705. Protein analysissoftware matches similar sequences using measure of homology assigned tovarious substitutions, deletions and other modifications, includingconservative amino acid substitutions. For instance, GCG containsprograms such as “Gap” and “Bestfit” which can be used with defaultparameters to determine sequence homology or sequence identity betweenclosely related polypeptides, such as homologous polypeptides fromdifferent species of organisms or between a wild type protein and amutein thereof. See, e.g., GCG Version 6.1.

A typical algorithm used comparing a molecule sequence to a databasecontaining a large number of sequences from different organisms is thecomputer program BLAST (Altschul, 1990; Gish, 1993; Madden, 1996;Altschul, 1997; Zhang, 1997), especially blastp or tblastn (Altschul,1997). Typical parameters for BLASTp are: Expectation value: 10(default); Filter: seg (default); Cost to open a gap: 11 (default); Costto extend a gap: 1 (default); Max. alignments: 100 (default); Word size:11 (default); No. of descriptions: 100 (default); Penalty Matrix:BLOWSUM62.

When searching a database containing sequences from a large number ofdifferent organisms, it is typical to compare amino acid sequences.Database searching using amino acid sequences can be measured byalgorithms other than blastp known in the art. For instance, polypeptidesequences can be compared using FASTA, a program in GCG Version 6.1.FASTA provides alignments and percent sequence identity of the regionsof the best overlap between the query and search sequences (Pearson,1990, hereby incorporated herein by reference). For example, percentsequence identity between amino acid sequences can be determined usingFASTA with its default parameters (a word size of 2 and the PAM250scoring matrix), as provided in GCG Version 6.1, hereby incorporatedherein by reference.

In certain embodiments, a metabolic pathway converts a carbon source toa desired intermediate or end product. For example, a carbon source canbe converted to pyruvate, which can be metabolized to acetyl-CoA to PHBor isoprene. Suitable carbon sources can be sugars. For example, acarbon source can be a biomass derived sugar. A “biomass derived sugar”includes, but is not limited to, molecules such as glucose, sucrose,mannose, xylose, and arabinose. The term biomass derived sugarencompasses suitable carbon substrates of 1 to 7 carbons ordinarily usedby microorganisms, such as 3-7 carbon sugars, including but not limitedto glucose, lactose, sorbose, fructose, idose, galactose and mannose allin either D or L form, or a combination of 3-7 carbon sugars, such asglucose and fructose, and/or 6 carbon sugar acids including, but notlimited to, 2-keto-L-gulonic acid, idonic acid (IA), gluconic acid (GA),6-phosphogluconate, 2-keto-D-gluconic acid (2 KDG), 5-keto-D-gluconicacid, 2-ketogluconatephosphate, 2,5-diketo-L-gulonic acid,2,3-L-diketogulonic acid, dehydroascorbic acid, erythorbic acid (EA) andD-mannonic acid.

Cellulosic and lignocellulosic feedstocks and wastes, such asagricultural residues, wood, forestry wastes, sludge from papermanufacture, and municipal and industrial solid wastes, provide apotentially large renewable feedstock for the production of chemicals,plastics, fuels and feeds. Cellulosic and lignocellulosic feedstocks andwastes, composed of carbohydrate polymers comprising cellulose,hemicellulose, and lignin can be generally treated by a variety ofchemical, mechanical and enzymatic means to release primarily hexose andpentose sugars. These sugars can then be “fed” into a pathway to producepyruvate as further described herein.

The disclosure provides accession numbers for various genes, homologsand variants useful in the generation of recombinant microorganismdescribed herein. It is to be understood that homologs and variantsdescribed herein are exemplary and non-limiting. Additional homologs,variants and sequences are available to those of skill in the art usingvarious databases including, for example, the National Center forBiotechnology Information (NCBI) access to which is available on theWorld-Wide-Web.

Culture conditions suitable for the growth and maintenance of arecombinant microorganism provided herein are known in the art.

It is understood that a range of microorganisms can be engineered toexpress one or more enzymes of the disclosure. It is also understoodthat various microorganisms can act as “sources” for genetic materialencoding target enzymes suitable for use in a recombinant microorganismprovided herein.

The term “microorganism” includes prokaryotic and eukaryotic microbialspecies from the Domains Archaea, Bacteria and Eucarya, the latterincluding yeast and filamentous fungi, protozoa, algae, or higherProtista. The terms “microbial cells” and “microbes” are usedinterchangeably with the term microorganism.

The term “prokaryotes” is art recognized and refers to cells whichcontain no nucleus or other cell organelles. The prokaryotes aregenerally classified in one of two domains, the Bacteria and theArchaea. The definitive difference between organisms of the Archaea andBacteria domains is based on fundamental differences in the nucleotidebase sequence in the 16S ribosomal RNA.

The term “Archaea” refers to a categorization of organisms of thedivision Mendosicutes, typically found in unusual environments anddistinguished from the rest of the procaryotes by several criteria,including the number of ribosomal proteins and the lack of muramic acidin cell walls. On the basis of ssrRNA analysis, the Archaea consist oftwo phylogenetically-distinct groups: Crenarchaeota and Euryarchaeota.On the basis of their physiology, the Archaea can be organized intothree types: methanogens (prokaryotes that produce methane); extremehalophiles (prokaryotes that live at very high concentrations of salt([NaCl]); and extreme (hyper) thermophilus (prokaryotes that live atvery high temperatures). Besides the unifying archaeal features thatdistinguish them from Bacteria (i.e., no murein in cell wall,ester-linked membrane lipids, etc.), these prokaryotes exhibit uniquestructural or biochemical attributes which adapt them to theirparticular habitats. The Crenarchaeota consists mainly ofhyperthermophilic sulfur-dependent prokaryotes and the Euryarchaeotacontains the methanogens and extreme halophiles.

“Bacteria”, or “eubacteria”, refers to a domain of prokaryoticorganisms. Bacteria include at least 11 distinct groups as follows: (1)Gram-positive (gram+) bacteria, of which there are two majorsubdivisions: (1) high G+C group (Actinomycetes, Mycobacteria,Micrococcus, others) (2) low G+C group (Bacillus, Clostridia,Lactobacillus, Staphylococci, Streptococci, Mycoplasmas); (2)Proteobacteria, e.g., Purple photosynthetic+non-photosyntheticGram-negative bacteria (includes most “common” Gram-negative bacteria);(3) Cyanobacteria, e.g., oxygenic phototrophs; (4) Spirochetes andrelated species; (5) Planctomyces; (6) Bacteroides, Flavobacteria; (7)Chlamydia; (8) Green sulfur bacteria; (9) Green non-sulfur bacteria(also anaerobic phototrophs); (10) Radioresistant micrococci andrelatives; and (11) Thermotoga and Thermosipho thermophiles.

“Gram-negative bacteria” include cocci, nonenteric rods, and entericrods. The genera of Gram-negative bacteria include, for example,Neisseria, Spirillum, Pasteurella, Brucella, Yersinia, Francisella,Haemophilus, Bordetella, Escherichia, Salmonella, Shigella, Klebsiella,Proteus, Vibrio, Pseudomonas, Bacteroides, Acetobacter, Aerobacter,Agrobacterium, Azotobacter, Spirilla, Serratia, Vibrio, Rhizobium,Chlamydia, Rickettsia, Treponema, and Fusobacterium.

“Gram positive bacteria” include cocci, nonsporulating rods, andsporulating rods. The genera of gram positive bacteria include, forexample, Actinomyces, Bacillus, Clostridium, Corynebacterium,Erysipelothrix, Lactobacillus, Listeria, Mycobacterium, Myxococcus,Nocardia, Staphylococcus, Streptococcus, and Streptomyces.

Accordingly, the disclosure provides an in vitro or in vivo engineeredpathway that comprises an NADPH-dehydrogenase (e.g., an NADPH-PDH orhomolog thereof), an NADH-dehydrogenase (e.g., an NADPH-PDH or homologthereof), and an NADH-oxidase (e.g., an NOX or homolog thereof).

As previously discussed, general texts which describe molecularbiological techniques useful herein, including the use of vectors,promoters and many other relevant topics, include Berger and Kimmel,Guide to Molecular Cloning Techniques, Methods in Enzymology Volume 152,(Academic Press, Inc., San Diego, Calif.) (“Berger”); Sambrook et al.,Molecular Cloning—A Laboratory Manual, 2d ed., Vol. 1-3, Cold SpringHarbor Laboratory, Cold Spring Harbor, N.Y., 1989 (“Sambrook”) andCurrent Protocols in Molecular Biology, F. M. Ausubel et al., eds.,Current Protocols, a joint venture between Greene Publishing Associates,Inc. and John Wiley & Sons, Inc., (supplemented through 1999)(“Ausubel”), each of which is incorporated herein by reference in itsentirety.

Examples of protocols sufficient to direct persons of skill through invitro amplification methods, including the polymerase chain reaction(PCR), the ligase chain reaction (LCR), Qβ-replicase amplification andother RNA polymerase mediated techniques (e.g., NASBA), e.g., for theproduction of the homologous nucleic acids of the disclosure are foundin Berger, Sambrook, and Ausubel, as well as in Mullis et al. (1987)U.S. Pat. No. 4,683,202; Innis et al., eds. (1990) PCR Protocols: AGuide to Methods and Applications (Academic Press Inc. San Diego,Calif.) (“Innis”); Arnheim & Levinson (Oct. 1, 1990) C&EN 36-47; TheJournal Of NIH Research (1991) 3: 81-94; Kwoh et al. (1989) Proc. Natl.Acad. Sci. USA 86: 1173; Guatelli et al. (1990) Proc. Nat'l. Acad. Sci.USA 87: 1874; Lomell et al. (1989) J. Clin. Chem 35: 1826; Landegren etal. (1988) Science 241: 1077-1080; Van Brunt (1990) Biotechnology 8:291-294; Wu and Wallace (1989) Gene 4:560; Barringer et al. (1990) Gene89:117; and Sooknanan and Malek (1995) Biotechnology 13:563-564.

Improved methods for cloning in vitro amplified nucleic acids aredescribed in Wallace et al., U.S. Pat. No. 5,426,039.

Improved methods for amplifying large nucleic acids by PCR aresummarized in Cheng et al. (1994) Nature 369: 684-685 and the referencescited therein, in which PCR amplicons of up to 40 kb are generated. Oneof skill will appreciate that essentially any RNA can be converted intoa double stranded DNA suitable for restriction digestion, PCR expansionand sequencing using reverse transcriptase and a polymerase. See, e.g.,Ausubel, Sambrook and Berger, all supra.

The invention is illustrated in the following examples, which areprovided by way of illustration and are not intended to be limiting.

EXAMPLES

Materials.

Miller LB media or Miller LB-agar (BD Difco) was used for growth ofbacterial strains in liquid or solid media. E. coli BL21Gold(DE3) [B,F-, ompT, hsdS_(B), (r_(B)-,m_(B)-), dcm+, Tetr, galλ, (DE3) endA Hte](Agilent) was used as host for both cloning and expression ofrecombinant proteins using pET vectors. E. coli TOP10(DE3) [F-mcrAΔ(mrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 nupG recA1 araD139 Δ(ara-leu)7697 galE15 galK16 rpsL(Str^(R)) endA1 λ⁻] was used forexpression of recombinant proteins from the pBAD/p15A vector. PlasmidspET28a(+) and pET22b(+) were purchased from Novagen. HotStart TaqMastermix (Denville) was used for gene amplification from genomic orplasmid DNA. Phusion DNA polymerase (Finnizymes), Taq DNA ligase(MCLab), and T5 Exonuclease (Epicenter) were purchased separately andused to make the assembly master mix (AMM) used for cloning. ATP,(±)-α-lipoic acid, pyruvate, Coenzyme A, and NAD⁺ were from Sigma.

Plasmid Construction.

The expression plasmids for the PHB enzymes were constructed from thepET28a plasmid backbone using the Nde1 and Sac1 cut sites to produceconstructs with an N-terminal 6×His tag for purification. The genesencoding acetyl CoA acetyltransferase (phaA; YP_725941, the informationassociated with the accession number is incorporated herein byreference) and acetoacetyl-CoA reductase (phaB; YP_725942, theinformation associated with the accession number is incorporated hereinby reference) were amplified and cloned from R. eutropha genomic DNA.The gene encoding polyhydroxybutyrate synthase (phaC; HE_610111, theinformation associated with the accession number is incorporated hereinby reference) was synthesized and codon optimized for expression in anE. coli host before being subcloned into the pET28a expression vector.For the isoprene pathway, the constructs were the same as described inreference (Korman, T. P., Sahachartsiri, B., Li, D., Vinokur, J. M.,Eisenberg, D. and Bowie, J. U. (2014), “A synthetic biochemistry systemfor the in vitro production of isoprene from glycolysis intermediates.”Protein Science. doi: 10.1002/pro.2436).

E. coli BL21-Gold cells were used as the host strain for enzymeexpression. All enzymes were expressed in Luria-Bertani (LB) mediasupplemented with 50 μg/mL kanamycin and were induced with 0.2 mMisopropyl-β-D-1-thioglactopyranoside added to the culture at the end oflog phase growth. The phaA, phaB, MVK, PMVK, and IspS were induced at37° C. overnight and phaB, THL/HMGR, HMGS, and IDI were induced at 18°C. overnight. The phaC was induced at 25° C. for 5 hours beforeharvesting.

Enzyme Purification.

Cells from 0.5 L of culture were harvested by centrifugation andresuspended in 150 mM Tris pH 7.5, 100 mM NaCl. The cells were lysed onice with sonication and the cell debris was removed by 12,000×gcentrifugation at 4° C. The supernatant was then mixed with 5 mLnickel-nitrilotriacetic acid (NTA) agarose and after 30 minutes, theagarose slurry was loaded onto a gravity column and washed with fivecolumn volumes of 100 mM Tris pH 7.5, 100 mM NaCl, 15 mM imidazole. Theenzyme was then eluted with 250 mM imidazole, 100 mM Tris pH 7.5. Theresulting enzyme was dialyzed into 50 mM Tris pH 7.5, 50 mM NaCl andstored at 4° C.

Expression Vectors for PDH Subunits E1αβ, E2, and E3, and E. coli LplA.

The E1, E2, and E3 domains were all amplified separately from G.stearothermophilus genomic DNA (ATCC) using primers that contained 15-20bp complementary to the gene and 15-20 bp complementary to the multiplecloning site in the vector where the gene would be placed. The genesencoding E1α and E1β were amplified together from G. stearothermophilusgenomic DNA and cloned into pET28a(+) that had been digested with NcoIand XhoI. This created a tag-less construct for E1 expression undercontrol of the T7 promoter where E1α translation uses the RBS from thepET28 vector while E1β uses the endogenous RBS from G.stearothermophilus. The E2 and E3 domains were amplified separately andcloned into pET22b(+) digested with NdeI and XhoI or pET28a(+) digestedwith NcoI and XhoI respectively to create tag-less E2 and E3 constructs.The E. coli lipoate protein ligase, LplA, was amplified from E. coli K12genomic DNA and assembled into pBAD/p15A digested with XhoI and EcoRI tocreate 6×His-LplA.

Overexpression and Purification of G. sterothermophilus PDH Subunits andE. coli LplA.

All E. coli strains were grown at 37° C. in LB-media supplemented withappropriate antibiotic (100 μg/mL ampicillin, 50 μg/mL kanamycin, or 34μg/mL chloramphenicol). For all constructs, 5 mL of overnight starterculture was used to inoculate 1 L of LB-media. Once the OD₆₀₀ reached0.6, 0.3 mM IPTG (pET vectors) or 0.02% arabinose (pBAD/p15A) was addedto induce protein expression. After 16 hours, cells were harvested,resuspended (4 mL/g wet cells) in 50 mM Tris-Cl pH 7.5, 0.1 M NaCl(Buffer A), lysed by sonication, and cell debris removed bycentrifugation at 30,000×g for 20 min.

25 mL of the E. coli lysate containing 6×His-LplA was loaded onto a 3 mLNi-NTA resin (Qiagen), washed with 25 mL Buffer A containing 10 mMimidazole, and eluted with 5 mL Buffer A containing 250 mM imidazole.Pure 6×His-LplA was then stored at 4° C. until use.

The individual domains of G. stearothermophilus PDH were partiallypurified from E. coli lysates by heat prior to modification andreconstitution of the PDH complex. E1αβ, E2, or E3 containing lysateswere incubated at 65° C. for 35 minutes to heat denature E. coliproteins followed by centrifugation at 30,000×g for 20 min to pellet theprecipitated proteins. Nearly all of the PDH domains remain in thesupernatant. Next, the E2 domain was lipoated in the heated extract bythe addition of 1 mM (±)-α-lipoic acid, 2 mM ATP, 3 mM MgCl₂, and 50 μgof purified 6×His-LplA. The lipoation reaction was then allowed toproceed with gentle mixing overnight at 25° C., yielding lipoated E2(E2lip). After lipoation, E1αβ, E2lip, and E3 were mixed in a 3:1:3molar ratio and incubated for at least 1 hour at 25° C. to form theactive GsPDH complex. The GsPDH complex was then isolated byultracentrifugation (Beckman) for 4 hours at 95,000×g. The resultingyellow pellet was resuspended in 20 mM Tris-Cl, pH 7.5 in 1/50 thestarting volume and assayed for activity. SDS-PAGE analysis confirmedthe presence of all 4 domains and indicated that the preparationwas >90% pure. The reconstituted complex was stored at 4° C. until use.

Enzyme Activity and Optimization.

NoxE was assayed by monitoring the oxidation of NAD(P)H at 340 nm. Theassay was carried out in 100 mM tris-HCl pH 7.5, 5 mM MgCl₂, 5 mM KCl,and 0.2 mM NAD(P)H.

WT and mutant PDH were assayed by monitoring the reduction of NAD(P)⁺ at340 nm. The assay was carried out in 50 mM Tris pH 7.5, 5 mM MgCl₂, 5 mMpyruvate, 1 mM CoA, and 0.5 mM of NAD (P)+.

PhaC was assayed by monitoring the absorbance of the hydrolysis of thethioester bond of the substrate 3HBCoA at 235 nm. The assay was carriedout in 100 mM Tris pH 7.5, 5 mM MgCl₂ and 0.15 mM 3HBCoA.

Activity of isoprene pathway enzymes were measured as reportedpreviously (Korman et al.). The amount of each enzyme in thereconstituted isoprene pathway described below is show in Table A.

TABLE A List of the enzymes and activities used in the production of PHBor Isoprene from pyruvate. Enzyme Units/mg mg added Units added 1GsPDH^(NAD) 0.082 ± 0.007  0.002/0.0013 0.00016/0.00011  1′ GsPDH^(NADP)0.12 ± 0.008 0.076/0.0095 0.009/0.001 2 NoxE 0.35 ± 0.036  0.020/0.00625 0.007/0.0022 3 PhaA 76.2 ± 4.4  0.023 1.75 4 PhaB 6.1 ± 0.6  0.0140.085 5 PhaC 142.7    0.032 4.57 6 EfTHL-  0.06 ± 0.002^(a) 0.0030.00018 HMGR 7 EfHMGS^(b) 0.6 ± 0.01 0.041 0.025 8 EfHMGR  0.06 ±0.002^(a) 0.023 0.0014 9 ScMVK 47.0 ± 0.9  0.008 0.38 10  SsPMVK 0.8 ±0.02 0.029 0.023 11  ScMDC 4.0 ± .07  0.038 0.152 12  EcIDI 0.035^(c)0.083 0.003 13  PaIspS 0.156^(d) 0.088 0.014 ^(a)Assayed in forwarddirection (synthesis) by coupling to MvaS and monitoring NADPHconsumption

Final PHB Reaction Conditions and Analysis.

The optimized self-sustaining reaction for the biotransformation ofpyruvate to PHB was composed of 250 mM Tris pH 7.5, 5 mM MgCl, 5 mM KCl,0.5 mM CoA, 0.1 mM NAD⁺, 0.5 mM NADP⁺, 50 mM pyruvate, 2 μg PDH^(NA)DH,76 μg PDH^(NADPH), 23 μg phaA, 14 μg phaB, and 32 μg phaC in a finalreaction volume of 200 μL. The reactions were initiated with theaddition of pyruvate, which was left out of the initial mixture. All PHBreactions were performed at room temperature. For testing theautoregulatory behavior of the purge valve, some enzyme concentrationswere suboptimal: 5 μg phaA, 2.5 μg phaB, and 1.9 μg phaC.

To assay for PHB, the reactions were lyophilized and incubated with 1 mLchloroform, 0.45 mL methanol, and 0.05 mL H₂SO₄ to hydrolyze the polymerand generate methyl 3-hydroxybutyrate. The reactions were extracted with0.5 ml water and 1 μL of the chloroform layer was applied to a 0.25micron HP-Innowax column using a HP 5890 Series II gas chromatogram. TheGC method used an injection temperature that was held at 35° C. for 5minutes before it was increased to 275° C. over 40 minutes. The peakintensities were compared to an authentic standard to assessconcentrations.

Isoprene Reaction Conditions and Analysis.

In vitro production of isoprene was performed as described previously(Korman et al.) with the following changes. 200 μL reactions were set upin 2 mL gas tight vials containing enzymes, 3 mM pyruvate, 15 mM ATP,0.6 mM CoA, 0.2 mM NAD+, 0.4 mM NADP+(or 5 mM NADPH), 10 mM MgCl₂, 20 mMKCl, 0.1 mM thiamine pyrophosphate in 100 mM tris-Cl pH 8.5 andincubated at 32° C. for 18 hours. Isoprene production was monitored bydirect sampling of 100 μL the headspace using a 100 μL gas-tightsyringe. The headspace was analyzed by GC-FID (HP5980II) equipped with aGS-GasPro column (0.32 mm×30 m, Agilent). The amount of isopreneproduced was quantified by comparison to a standard curve of variousisoprene concentrations sampled in the same manner.

To implement the purge valve module, an NADP⁺-utilizing PDH was needed.A mutant of E. coli PDH has been engineered to have NADP⁺ specificity byintroducing mutations into the E3 enzyme (EcE3). The E. coli PDH was,however, unstable. A mutant of the thermophilic G. stearothermophilusPDH was engineered that preferentially accepts NADP⁺ with increasedenzyme stability.

Similar to design of the E. coli PDH mutant, the G. stearothermophilusPDH mutant (SEQ ID NO:7) was designed by overlaying the known structureof the G. stearothermophilus E3 subunit (GsE3) with the known structureof the related E. coli glutathione reductase, which utilizes NADP⁺. Thestructural superposition allowed for positioning the additionalphosphate moiety in the active site of the GsE3, based on how it wasplaced in glutathione reductase (see FIG. 2). The side chainsubstitutions were then designed in GsE3 that might allow acceptance ofthe phosphate. Guidance was identified from a prior successful design ofthe EcE3 enzyme which shares 47% sequence identity with the GsE3. Themutations introduced into EcE3 were E206V, G207R, A208K, G209H and S213R(GsE3 numbering). After examining the changes in the context of the GsE3structure, all were introduced but G209H, because it appeared that thenew His side chain might create steric clashes with nearby K224 and N237residues.

The kinetic properties of the engineered and wild-type enzymes revealthat the mutations alter specificity as desired. The kinetic parametersare listed in Table B. For the wild-type G. stearothermophilus enzyme(GsPDH^(NADH)), k_(cat) is 11.2 times higher with NAD⁺ than NADP⁺ andk_(cat)/K_(m) is 1150 times higher. For the engineered mutant(GsPDH^(NADPH)), k_(cat) is 7.3 times higher with NADP⁺ than NAD+ andk_(cat)/K_(m) is 21 times higher. Thus, we were able to flip thespecificity of the PDH enzyme.

TABLE B List of the catalytic properties of the purge valve enzymes.Enzyme K_(m) k_(cat) k_(cat)/ Name Substrate (mM) (μM/min/mg) K_(m)GsPDH − NAD+  0.013381 ± 0.00083 82.651 ± 0.66 6167.91 NAD+ NADP+  1.381± 0.41 7.3954 ± 0.85 5.36 Pyruvate 0.52736 ± 0.049 91.976 ± 1.9  174.40GsPDH − NADP+  0.157 ± 0.013 117.75 ± 8.1  750.00 NADP NAD+ 0.45269 ±0.178 16.104 ± 1.8  35.56 Pyruvate 0.42328 ± 0.068 174.3 ± 2.7 411.76NoxE NADH 0.074925 ± 0.026  348.57 ± 36.5 4653.81 NADPH 2.9515 ± 0.771.4009 ± 0.32 0.47

The GsPDH^(NADH) and GsPDH^(NADPH) enzymes (henceforth designatedPDH^(NADH) and PDH^(NADPH)) were much more stable than their E. colicounterparts. As shown in FIG. 7, the G stearothermophilus enzymesretained ˜50% activity after one hour incubation at 67° C. whereas theE. coli PDH enzymes were completely inactivated at 50° C.

A second aspect of the purge valve design is the use of an NADH oxidasewith high cofactor specificity. NoxE from L. lactis was selected as itis a water forming NADH oxidase so it doesn't generate any toxicproducts such as hydrogen peroxide. As shown in Table B, the K_(cat) ofNoxE is 248.8 times greater with NADH than NADPH and k_(cat)/K_(m) is9900 times greater.

The enzymes chosen for the various experiments are listed in Table C. Inthe initial tests only the wild type, PDH^(NADH) complex and NoxE wasused to generate Acetyl-CoA and NADPH was supplied exogenously. Afteroptimizing enzyme ratios in this system, the mutant PDH^(NADPH) wasadded to test in situ generation of NADPH. Finally, the amount ofPDH^(NADPH) was optimized, keeping the other enzymes fixed.

Enzyme Name Accession Number Plasmid Tag Organism Purge Valve 1PDH^(NADH) Pyruvate Dehydrogenase Complex G. stearothermophilus  1′PDH^(NADPH)  1a E1a Pyruvate Dehydrogenase Subunit a P21873 pET28 noneG. stearothermophilus (SEQ ID NO: 1)  1b E1b Pyruvate DehydrogenaseSubunit b P21874 pET28 none G. stearothermophilus (SEQ ID NO: 2)  1c E2Dihydrolipoamide Acetyltransferase CAA37630 pET22 none G.stearothermophilus (SEQ ID NO: 3)  1d E3^(NADH) DihydrolipoamideDehydrogenase P11959 pET28 none G. stearothermophilus (SEQ ID NO: 5)  1′d E3^(NADPH) Mutant Dihydrolipoamide P11959 pET29 none G.stearothermophilus Dehydrogenase (SEQ ID NO: 7)  1e LplA Lipoate ProteinLigase NP_418803 pBAD/p15A N-His E. coli (SEQ ID NO: 8) 2 NoxE NADHoxidase (H20 forming) YP_007507681 pET22 C-His L. lactis (SEQ ID NO: 10)PHB Pathway 3 PhaA Acetyl-CoA acetyltransferase GJUJ-1435 pET28 N-His R.eutropha (SEQ ID NO: 11) 4 PhaB 3-hydroxybutryl-CoA reductase GJUJ-1436pET28 N-His R. eutropha (SEQ ID NO: 12) 5 PhaC Polyhydroxybutyratesynthase G8BLJ2 pET28 N-His C. necator sp. S-6 (SEQ ID NO: 13) IsoprenePathway 6 THL/HMGR Thiolase/HMG-CoA Reductase fusion WP_002357755 pET28N-His E. faecalis (SEQ ID NO: 14) 7 HMGS HMG-CoA Synthase A110G MutantWP_010785222 pET28 N-His E. faecalis (SEQ ID NO: 15) 8 HMGR HMG-CoAReductase WP_002357755 pET28 N-His E. faecalis (SEQ ID NO: 16) 9 MVKmevalonate kinase BAA24409 pET28 N-His S. cerevisiae (SEQ ID NO: 17) 10 PMVK phosphomevalonate kinase NP_344303 pET28 N-His S. solfataricus (SEQID NO: 18) 11  MDC diphosphomevalonate decarboxylase NP_014441 pET28N-His S. cerevisiae (SEQ ID NO: 19) 12  Idi isopentenyl diphosphateisomerase NP_417365 pET22 C-His E. coli (SEQ ID NO: 20) 13  IspSIsoprene Synthase Q50L36 pET28 N-His P. alba (SEQ ID NO: 21)The sequences associated with the foregoing accession numbers areincorporated herein by reference. The SEQ ID NOs set forth above providethe polypeptide sequences. The coding sequences are readily available toone of skill in the art.

The progress of the optimized pyruvate to PHB reaction is shown in FIG.3 along with a control lacking the last enzyme, phaC. Both reactions hada PDH^(NADPH):PDH^(NADH) ratio of 40:1. At this ratio, the NADPH levelsrise rapidly (A₃₄₀) and are maintained throughout the time course (NoxErapidly oxidizes NADH so changes in A₃₄₀ reflect only changes in NADPHlevels). At the same time, PHB granules are produced as monitored byA₆₀₀ ³⁶.

PHB production was assayed using a gas chromatography method and foundthat the optimized reaction produced 2.45±0.5 mg/mL of PHB from 50 mMpyruvate which represents nearly complete conversion (94±20%) ofpyruvate to plastic. In the optimized system, 0.5 mM NADP⁺ wereinitially used, so achieving 94% yield requires over 90 turnovers of theNADP⁺ cofactor, indicating a high level of system sustainability.

The stability of the full system was assessed by mixing componentstogether and then initiating the reaction at various time delays. Thedecrease in extent of the reaction is shown in FIG. 8. The extent ofreaction remains 50% after two days.

The regulatory behavior of the purge valve is better seen at sub-optimalenzyme concentrations and ratios of PDH^(NADPH) to PDH^(NADH) that slowdown the response time. In the optimized assay (40:1 mole ratio ofPDH^(NADPH):PDH^(NADH)), a rapid rise in NADPH levels was observed,which was sustained throughout. In the non-optimal systems shown in FIG.4, the purge valve cannot respond as rapidly to drops in NADPHconcentrations so variations in NADPH levels were observed as the systemdevelops. We still observe a rapid initial rise in NADPH levels, but asintermediates build up, the consumption starts to outstrip NADPHproduction. Eventually, the system compensates by generating higherlevels of NADPH.

To test whether the system was robust to changes in cofactor levels, theinitial cofactor concentrations were varied in the reactions and theyields of PHB were measured. Each reaction was constructed withcombinations of NAD⁺, NADH, NADP⁺ or NADPH at either 0.1 mM or 1 mM andthe production of PHB was monitored by the final OD at 600 nm. All ofthe reaction conditions were compared to the optimized reaction thatproduced nearly complete conversion of pyruvate to PHB and were withinrandom variation. This result indicates that the purge valve cancompensate readily for changes in cofactor concentrations and reductionstates.

To test the versatility of the molecular purge valve and whether it canbe applied as a general platform for the production of a diverse arrayAcetyl-CoA derived compounds the PDH purge valve was used to produceisoprene via the Acetyl-CoA dependent mevalonate pathway. Korman et al.previously described the in vitro production of isoprene from pyruvate,which required the use of exogenously added NADPH. Similar to the PHBpathway the mevalonate pathway has an inherently different carbon andcofactor stoichiometry. In particular, the mevalonate pathway requires 3Acetyl-CoA and 2 NADPH for the production of isoprene (see FIG. 6A).Thus, system sustainability requires generation and regulation of NADPHlevels.

Experiments were performed to test whether the purge valve system canreplace exogenously added NADPH in the production of isoprene. As shownin FIG. 6B, the full purge valve system produces an 88.2±8.4% yield from3 mM pyruvate. This yield is even higher than the 81.4±2.0% yieldobtained if we add NADPH exogenously (FIG. 6B). If any of the purgevalve components (PDH^(NADPH), PDH^(NADH) or NoxE) were left, yields aredramatically reduced. Thus, the purge valve system is transportable toother synthetic biochemistry systems.

A number of embodiments of the invention have been described.Nevertheless, it will be understood that various modifications may bemade without departing from the spirit and scope of the invention.Accordingly, other embodiments are within the scope of the followingclaims.

What is claimed is:
 1. A recombinant, artificial or engineered metabolicpathway comprising a plurality of enzymatic steps that converts asubstrate to a product, wherein the pathway produces an unbalancedproduction of a cofactor, said pathway comprising: a firstcofactor-dependent enzyme that is capable of converting a firstsubstrate to a second substrate, said enzyme producing the unbalancedproduction of a cofactor; and a second cofactor-dependent enzymecomprising an NADH or an NADPH oxidase that recycles the cofactor. 2.The recombinant, artificial or engineered pathway of claim 1, whereinthe co-factor is an oxidizing/reducing co-factor.
 3. The recombinant,artificial or engineered pathway of claim 2, wherein theoxidizing/reducing co-factor is selected from the group consisting ofNAD⁺/NADH, NADP⁺/NADPH and FAD⁺/FADH.
 4. The recombinant, artificial orengineered pathway of claim 1, wherein the cofactor comprises NAD⁺/NADHor NADP⁺/NADPH.
 5. The recombinant, artificial or engineered pathway ofclaim 1, wherein the first cofactor-dependent enzyme comprises an NADHor an NADPH dehydrogenase.
 6. The recombinant, artificial or engineeredpathway of claim 5, wherein the NADH dehydrogenase is a NADH pyruvatedehydrogenase complex.
 7. The recombinant, artificial or engineeredpathway of claim 6, wherein the NADH pyruvate dehydrogenase complexcomprises a pyruvate dehydrogenase subunit a, a pyruvate dehydrogenasesubunit b, a dihydrolipoamide acetyltransferase, and a dihydrolipoamidedehydrogenase.
 8. The recombinant, artificial or engineered pathway ofclaim 7, wherein the pyruvate dehydrogenase subunit a comprises asequence that has at least 90% sequence identity to SEQ ID NO: 1,wherein the pyruvate dehydrogenase subunit b comprises a sequence thathas at least 90% sequence identity to SEQ ID NO: 2, wherein thedihydrolipoamide acetyltransferase has at least 90% sequence identity toSEQ ID NO: 3, and wherein the dihydrolipoamide dehydrogenase has atleast 90% sequence identity to SEQ ID NO: 5, wherein the complexconverts pyruvate to acetyl-CoA.
 9. The recombinant, artificial orengineered pathway of claim 7, wherein the pyruvate dehydrogenasesubunit a comprises a sequence that has at least 90% sequence identityto SEQ ID NO: 1, wherein the pyruvate dehydrogenase subunit b comprisesa sequence that has at least 90% sequence identity to SEQ ID NO: 2,wherein the dihydrolipoamide acetyltransferase has at least 90% sequenceidentity to SEQ ID NO: 3, and wherein the dihydrolipoamide dehydrogenasehas at least 90% sequence identity to SEQ ID NO: 7 and preferentiallyuses NADP⁺, wherein the complex converts pyruvate to acetyl-CoA.
 10. Therecombinant, artificial or engineered pathway of claim 5, wherein theNADPH dehydrogenase is a member of a NADPH pyruvate dehydrogenasecomplex.
 11. The recombinant, artificial or engineered pathway of claim10, wherein the NADPH pyruvate dehydrogenase complex comprises apyruvate dehydrogenase subunit a, a pyruvate dehydrogenase subunit b, adihydrolipoamide acetyltransferase, and a mutant dihydrolipoamidedehydrogenase the preferentially uses NADP⁺.
 12. The recombinant,artificial or engineered pathway of claim 1, wherein the NADH or theNADPH oxidase is a NoxE or homolog thereof.
 13. The recombinant,artificial or engineered pathway of claim 12, wherein the NADH or theNADPH oxidase comprises a sequence that has at least 50% sequenceidentity to SEQ ID NO:
 10. 14. The recombinant, artificial or engineeredpathway of claim 1, wherein the pathway is in a cell-free system. 15.The recombinant, artificial or engineered pathway of claim 1, whereinthe pathway is in a living cell.
 16. The recombinant, artificial orengineered pathway of claim 1, wherein the recombinant, artificial orengineered pathway produces PHB.
 17. The recombinant, artificial orengineered pathway of claim 1, wherein the recombinant, artificial orengineered pathway produces ethanol.
 18. The recombinant, artificial orengineered pathway of claim 1, wherein the recombinant, artificial orengineered pathway produces lactate.
 19. An enzymatic system comprisinga metabolic pathway including a plurality of enzymes for converting asubstrate to a product, the metabolic pathway having an unbalancedutilization of reducing/oxidizing cofactors, wherein the enzymaticsystem comprises a metabolic purge valve comprising an NADH pyruvatedehydrogenase and a NADH/NADPH oxidase.
 20. A recombinant polypeptidecomprising a sequence that has at least 99% sequence identity to SEQ IDNO: 5 and comprising the mutations E206V, G207R, A208K, and S213R,wherein the polypeptide has dihydrolipoamide dehydrogenase activity.